SDIWG:Meeting Minutes 20080222

Agenda: NCBC Joint Working Group Meeting

Top page of SDIWG web site

Notes

Friday February 22, 2008: 2:30 -- 3:30 PM EST
Please contact Peter Lyster for information Peter Lyster
SDIWG Meetings Page
Save the date for the next SDWIG tcon/Connect, three months from now: Friday May 16, 2008

Tcon DRAFT Agenda

• Roll Call/Note-taker (Henry Chueh) (5 min)
• Minutes from most recent SDIWG tcon Nov 16, 2007 (5 min)
• NCBC All Hands Meeting, August 13-15, 2008. Planning & Brainstorm discussion (Peter, Karin, All)
• Status check on three working groups: Biositemaps Resourceome, Scientific Ontologies, NCBC Driving Biological Projects Interactions and Impact
• Demo on Biomedical Resource Ontology (see BRO Requirements document) (Daniel Rubin). The demo will describe a stable development environment for the BRO and repository in BioPortal. This is a key component of the Biositemaps effort.
  • Overview of white paper (‘the biositemaps concept’) (Daniel, Ivo, Peter)
  • Overview of (i) collaborative development environment for BRO and (ii) BioPortal repository of BRO (how is BRO accessed through API?) (Daniel)
  • Overview of how iTools accesses the current corpus of three proto-biositemaps (google”filtetype:xml biositemap”). (Ivo)
  • Overview of plan for next 2 to 4 months (Peter)
    • (1) In the next two months NCBO develops a stable platform for content development and content repository in bioportal relating to the resource ontology, culminating in ½ to 1 day tcon with authorized seven Center reps to finalize v1.0 resource ontology (I may add rep from NITRC and NIF, Bill Bug). NCBO is generating and executing the plan for the ‘stable platform’
    • (2) After that Lyster contacts each PI and get personal commitment to create biositemaps.xml content on their web sites.
• Upcoming meetings: AMIA translational, Zac, ...
• Next 2 meeting date (Friday May 16 2:30 PM ET and three months after that)
• Questions/Information Sharing

Minutes

Note taker: (Peter Lyster) [Suggested order of note takers for future meetings: Chueh (this one); Sherman; Schroeder; Floratos; Rubin; Jags, Dinov]

• Review of November 16, 2007 Minutes
• Attendees: Daniel Rubin, Ivo Dinov, Karen Skinner, Karin Remington, David Kennedy, Olivier Bodenreider
  • Daniel showed Biomedical Resource Ontology (BRO) and other ontologies/terminologes (e.g., NCI Thesaurus) in Bioportal
  • Daniel described the link between the BRO and Ontrez which is the NCBO tool for curated indexing of resources (this uses the terminologies, including BRO that are in Bioportal); Daniel shows the Mapping capability
  • There was a general discussion of the development environment for the BRO—currently it exits as (i) the primary content is in Daniel’s private repository (CVS) (thus the full complement of old versions are not propagated into BioPortal, although BioPortal does show the difference between the current and immediately previous version); (ii) annotations that can be entered directly into Bioportal.
  • Daniel will put the current BRO on a Stanford gforge where it can be used by the NCBC SDIWG contacts to agree on a common BRO.
  • Daniel will write (and insert into the minutes) a brief description for immediate conversion from biositemaps based on xml to biositemaps based on owl.
• Go over dates for next year's meetings:
  • AMIA Summit on Translational Bioinformatics, San Francisco, http://www.amia.org/inside/releases/2007/translationalbioinformaticssummit_pr2007.pdf, March 10-12 2008
  • Health Informatics April 11, 2008, Boston, MA - Health Informatics (Zak?) Need a link.
  • NCBC All Hands Meeting, date August 13-15, Bethesda
  • SDWGI meets once every 3 months 11:30 AM (Pacific), third Fri of the month.

Action Items

• Convert Biositemaps method to owl
• Convene SDIWG tcon (probably lasting 1/2 day to agree on a common BRO)

Appendix: Biositemaps white paper

• Biositemaps Resourceome (Ivo Dinov, Daniel Rubin, Will Schroeder, Beth Kirschner, Karen Skinner, Zohara Cohen, Bill Bug, Peter Lyster)
  • The biositemaps white paper presents description of prototype for distributed architecture to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining software tools and information resources on the Internet. Each site which intends to contribute to the inventory instantiates a file on its Internet site ‘biositemap.xml’ which conforms to a defined schema and is tagged by a resource ontology. The prototype schema may be found at http://www.ncbcs.org/biositemaps/biositemaps-v04.xsd A good reference for XML editors is at http://en.wikipedia.org/wiki/Xml_editor e.g., we are using XMLmind. The prototype resource ontology may be found at http://bioontology.org/projects/ontologies/SoftwareOntology/
  • The Biomedical Resource Ontology (BRO) (see BRO Requirements document) is an extensible terminology for online electronic resources, intended to be an enabling technology for tools which improve query and access to online resources.
  • Further postings will be made at the NCBC portal at http://www.ncbcs.org/biositemaps/
  • Status of the NCBC iTools, which is uses the biositemaps. http://iTools.loni.ucla.edu